Calculate surfaces thickness
Raycasting from inner to outer

Code to shoot a ray from each inner object face centre along the normal, to the outer object.  Object.ray_cast(...) the parameters need to be in the local space of the object we are casting on.

Some notes. The code below gives expected result for a cube within a cube, or sphere within a sphere, as the face normal is the same direction (with origin at centre of geom) as face.centre - origin.   For your object, might want to have some test where normal isn't in the direction of closest point on outer.  For example on the slope of bumps. (hope that's not too confusing)

import bpy
context = bpy.context
scene = context.scene
show_hit = True # add empty at hit.

def draw_empty_arrow(loc, dir, draw_size=1):
    R = (-dir).to_track_quat('Z', 'X').to_matrix().to_4x4()
    mt = bpy.data.objects.new("mt", None)
    R.translation = loc + dir
    #mt.show_name = True 
    mt.matrix_world = R
    mt.empty_draw_type = 'SINGLE_ARROW'
    mt.empty_draw_size = dir.length
    scene.objects.link(mt)

# check thickness by raycasting from inner object out.
# select inner and outer obj, make inner active
inner_obj = context.active_object
outer_obj = context.selected_objects[1]
omwi = outer_obj.matrix_world.inverted()

imw = inner_obj.matrix_world
omw = outer_obj.matrix_world
mat = omwi * imw
hits = [] # vectors from inner to outer
for face in inner_obj.data.polygons:
    print("face", face.index)
    o = mat * face.center
    n = mat * (face.center + face.normal) - o
    hit, loc, norm, index = outer_obj.ray_cast(o, n)
    if hit:
        print("hit outer on face %d" % index)
        hits.append((o, loc))

# test on cube, cylinder ok.
# print((outer_obj.dimensions.x - inner_obj.dimensions.x) / 2)
if hits:        
    avge_thickness = sum((omw * hit - omw * o).length for o, hit in hits) / len(hits)
    print(avge_thickness)  
    if show_hit:
        for hit, o in hits:
            draw_empty_arrow(omw * o, omw * hit - omw * o, draw_size=1)



Result of running on sphere within a sphere (the outer sphere is wireframe)  Empties drawn from inner face to outer hit.